As I was browsing through the posts from 2005, I noticed that there was a rather protracted and intense debate between Asif (MysterAsif) and Saif (Saif6) in the post ?Possible sociological effects of TOE?? Although the original article was on sociological effects of evolution, the comments, about halfway through the discussion, diverged into a serious assessment of the actual theory of evolution. It is my utmost pleasure to use the second half of that discussion to show that the emperor has no clothes. And, in a scientific and rational manner, I shall do so by stripping, piece by piece, the key evolutionist arguments. But it is not my aim to dwell at length on evolution?s sociological ramifications, including a causal connection with communist ideologies, even though the issues are undeniably significant enough to warrant serious examination in the wider social spheres. Accordingly, I had largely ignored the post up to now by assuming, from the title of the post, that the discussion is not pertinent to analysis of scientific and theoretical basis for evolution and intelligent design. However, now that I have dug through the discussion, it seems that it would be a more efficient use of my subscription to Naseeb and a more stimulating and delicious exercise to dissect the scientific and the rational foundations, or lack thereof, of the evolutionist paradigm. Since I intend to strictly confine my rebuttal to the scientific framework of evolution, I started this new thread, which I have kept textually separate from, yet wholly dependent on, the original trail of comments ignited with the article on sociological effects of evolution.

I have collected in topical categories the comments that I want to respond to. Part 1 of this defense will discuss speciation, macroevolution, peer-review, and purported evidence for evolution. I apologize for the extent of this writing. Like biochemistry, which is ?in the details,? the argument of intelligent design theory (hereafter truncated IDT) is a thorough examination of positive evidence for design and a detailed dissection of the evolutionary argument.

Speciation and Macroevolution

To begin, a definition of ?species? and a rehash of the process of ?speciation? would be fruitful. A species is defined as ?a population or group of populations whose members have the potential to interbreed with one another in nature to produce viable, fertile offspring, but who cannot produce viable, fertile offspring with members of other species? (Campbell and Reece 465). The species concept emphasizes reproductive isolation. Obviously, speciation then is the process by which new species arise or, in other words, the process by which a single species, members of which were initially inter-breeding, becomes reproductively isolated. A few mechanisms of speciation that have been proposed are allopatric speciation (a geographic barrier such a mountain range leads to speciation), adaptive radiation (a subset of allopatric speciation, whereby several species arise from a common ancestor), and sympatric speciation (speciation that arises within the range of parent populations rather than in geographically isolated populations).

Is speciation considered macroevolution? Since speciation is ?at the boundary of microevolution and macroevolution? speciation is clearly not macroevolution proper (Campbell and Reece 476). The authors further pin the distinction between speciation and macroevolution in that the ?cumulative change during the millions of speciation episodes over vast tracts of time must account for macroevolution ?? (476). Thus, reproductive isolation of species or speciation is not macroevolution or evidence thereof. Does IDT claim that evolution lacks sufficient empirical evidence for speciation? No, because speciation has been observed in the wild and, in fact, Diane Dodd experimentally demonstrated the artificial speciation of Drosophila pseudoobscura fruit flies by adaptive radiation (1308-1311).

So far, it has not been firmly established, from the vantage of the cell?s genetic and biochemical processes, the precise point at which a certain evolutionary transformation allegedly crosses the fuzzy line from microevolution onto macroevolution. Although speciation is one marginal stride in stepping from microevolution toward alleged macroevolution, current scientific understanding has not offered a precise and clear-cut characterization of macroevolution at the level of the cell?s genetic and biochemical processes. That is why the statement, ?The theory of evolution has not accounted for macroevolution? is analogous to the statement, ?The theory of evolution has not accounted for XYZ.? But it is legitimate to ask, ?What exactly is XYZ?? Still, it is reasonable to confine the usage of the word ?macroevolution? to broader levels of transformations (e.g., fish to reptile to bird to mammal transformations). For a general transformation beyond mere speciation, a meticulous biochemical and genetic characterization of what precisely constitutes macroevolution has not been forthcoming, however.

To avoid such semantic obscurity of ?macroevolution? in the expression, ?The theory of evolution has not accounted for macroevolution,? where ?macroevolution? is not exclusively confined to its broader sense, I suggest that proponents of IDT instead state that the theory of evolution has not accounted for the origin of the information (Dembski?s complex specified information) necessary to produce novelty or innovation and that intelligent design is a more plausible explanation for the origin of biological information and higher taxa. The key words are information and novelty. Just a couple of examples of novelty or innovation are bird flight and dolphin sonar. A historic instance of the appearance of such information and novelty is the appearance of higher taxa during the Cambrian Explosion from 543 to 525 million years ago when many morphologically novel phyla and body plans arose in a geologically brief period of time and with ?no clear morphological antecedents in earlier Vendian or Precambrian fauna? (Meyer 215). The Burgess Shale in British Columbia, Canada is a well-known fossilized preservation of the innovative diversity of the Cambrian fauna.

>> Macroevolution, however, is claimed to be responsible for emerging a new species from an existing one. Interestingly enough this process has NEVER been observed and there exists absolutely no data backing its existence, yet, it?s been taught in our schools as an established fact? -Asif

I concede the essence of the reasoning, but let me tweak the semantics a bit to strengthen the argument. An emergence of a new species is not necessarily macroevolution. The reproductive isolation of a parent species results in the emergence of two or more new species, a process called speciation, not macroevolution. As shown above, speciation is not macroevolution in the most stringent sense. It is more accurate for the proponents of IDT to instead state that the origin of the complex specified information necessary to produce novelty or innovation has been neither observed in the wild nor empirically verified. I concur that there is no empirical data to substantiate the emergence of information needed to produce novelty in lifeforms and that the unsubstantiated gospel is nonetheless being taught in schools as if it is a well-tested scientific theory.

>> What ID criticizes, however, are the claims that a species acquiring a brand new feature (human growing wings to fly or an organism that contains absolutely no light sensitive cells end up with eyes etc.) without any help of design or intelligence. ?Asif

Better phrased! That is precisely what IDT criticizes.

>> Last, I am familiar with the difference between macroevolution and microevolution. ?Saif

If you had been really familiar with the distinction, you would not have made the erroneous comment below.

>> In fact, macroevolution (not just microevolution) has indeed been observed in nature. Experiments with fruit flies have generated reproductively isolated sub-groups, as have studies of displaced cichlid fishes in African lakes. ?Saif

Speciation, which has been observed and verified, is not macroevolution. The experiments with fruit flies and cichlid fishes have generated reproductively isolated species, a process called speciation, which is distinct from macroevolution. Speciation has not been shown to produce the information needed to generate novelty such as bird flight, dolphin sonar, and bat echolocation, and novelty along the lines of which arose during the Cambrian Explosion. It has not been empirically shown how novel anatomical structures and physiological functions might arise by purely naturalistic means. Even after reproductive isolation, a fruit fly still remains a fruit fly and a fish still remains a fish.

Instead of tinkering with fruit flies that remain fruit flies, perform an experiment to transform a fish into a reptile. Or, produce a novel design such as bat echolocation, which is being mimicked to design adaptive cruise controls and anti-collision detectors in vehicles, the design of which is called ?technological innovation? after which NASDAQ technology stocks rally in hysterical fireworks. Or, demonstrate how naturalistic mechanisms might produce the human brain?s parallel information processing system, which is being mimicked to design neural networks for artificial intelligence. Or, produce the likes of a lung, which is being used to enhance fuel cell optimization. Or, evolve an insect after which the ?innovative? idea of Mars-exploring robotic insects has been generated. Demonstrate in detail and with thoroughly meticulous experimentation how naturalistic mechanisms can achieve an innovative solution to a constraint-driven optimization problem to compromise between competing objectives in the external world. The story of Drosophila and cichlid fishes is primordial history.

>> Secondly, assuming you equate macroevolution with speciation, I found a nice listing of documented, observed cases of speciation: www.talkorigins.org ?Saif

Thank you, but the documented cases are instances of speciation, not macroevolution, as clarified above.

>> What other explanation could one arrive to, if the new species were no longer able to breed with their geographically isolated cousin species or parent species, but they were still able to breed with members of their own population? If this isn't speciation, then pray tell, what is? -Saif

Of course, it is speciation. At the same time, it is not macroevolution.

>> Anyway, macroevolution is founded primarily on inferential evidence that DOES exist even though we cannot directly observe large scale changes due to the time scales involved... -Saif

A logically justified inference is a valid scientific method of investigation even if certain phenomena cannot be directly observed. However, speciation does not warrant the inference of macroevolution since, for the reasons explained above, the inference is logically unjustified.

>> You did not respond to my question about what prevents the branched subgroups from breeding with one another if they share the same genomes. -Saif

Justify why it is logically pertinent to the logistical structure of my rebuttal that I respond to that question.

>> And since you define speciation the same way, then you admit that speciation can occur naturalistically? -Saif

Of course, speciation can happen naturalistically. And artificial speciation can also be engineered as was done in 1989 (Dodd 1308-1311).

>> What does speciation classify under... micro or macroevolution? -Saif

None, since speciation is ?at the boundary of microevolution and macroevolution? (Campbell and Reece 476). Refer to the introductory preface about speciation.

>> All evolutionary changes are gradual... observed speciation is not going to result in massive changes, but if you think that this subtle form of speciation is possible, then when you have hundreds of millions of years to work with, I think it's reasonable to accept that larger-scale changes are at least possible, especially when the rest of the inferential evidence falls in line with that view. ?Saif

Hidden in the hand-waving phrase ?larger-scale changes? is a gargantuan and a desperate attempt to save the theory from the plaguing problems explained above: the origin of the information required to produce novelty or innovation. Instead of shouting a hand-waving cry of a tooth fairy, evolutionists have been invited to demonstrate how naturalistic methods might produce these ?larger-sale changes,? which, in essence, are innovative solutions to constraint-driven optimization problems that require a compromise between competing objectives. I apologize for being such a dim-witted imbecile and for not exercising my naturalistically engendered creative intelligence, so please illustrate in detail, as you would to an idiot, how it is ?reasonable to accept? that these innovative optimization solutions might crack into existence by naturalistic means and how it is ?at least possible? to creatively imagine (like I do a folk tale of Santa Claus) that the solutions might somehow arise by naturalistic means.

>> If only direct evidence works for you, perhaps you should disavow knowledge of the existence of quarks (constituents of protons, neutrons, etc) since they have never been observed --- their existence has been indirectly inferred. Yet they are a cornerstrone of the Standard Model of particle physics. ?Saif

I am afraid that this is an argument by false analogy. The standard model and quantum field theory, of which the standard model is a subset, are mathematically intensive theories backed up with rigorous experimentation, the like of which is nowhere close to the non-mathematical, untested, and unsupported evolutionist assertion that naturalistic processes can produce the information needed to make innovative features. The theoretical framework and scientific predictions of the standard model, and indeed of physics in general, are corroborated with painstaking experimentation in the lab even if certain phenomena such as sub-atomic particles cannot be directly observed. For instance, in 1995 Fermilab?s Tevatron high-energy particle accelerator collided protons and anti-protons to produce top quarks, which were predicted by the standard model www.fnal.gov). But until such particles are produced in the lab or otherwise empirically confirmed to exist, the dogmatic gospel, which preaches that scientific findings of a well-tested theory have confirmed the existence of the particles, is not shoved down the throats of high school teenagers and the uninformed masses.

Refer to Fermilab?s list of key experiments and discoveries in particle physics, which is the subject of study of the standard model www.fnal.gov). Has the like of such experiments or tests been implemented to substantiate the claim that naturalistic processes can produce the information needed to create novelty? No.

Physics and astronomy employ mathematical equations in the theoretical framework, rigorous experimentation in the lab, and meticulous observation in the field to prove out scientific hypotheses, theories, and predictions. These sciences are described characteristically by mathematical equations. Evolutionary biology, however, employs little abstract mathematical reasoning. The controversial claims of evolutionary biology, therefore, cannot be compared to the theoretical framework of mathematically intensive subjects such as physics and astronomy. It is not comparing apples to apples. Yet, evolutionists are fond of arguing by analogy with theories such as Newton?s theory of gravitation. Such analogies are misleading.

>> My question was how ID can account for this observed speciation. Obviously it cannot. I suppose shoving the issue under the table is the easiest way of dealing with it. ?Saif

I do not see the relevance of this question to the subject matter of my rebuttal. Why is it relevant whether IDT can account for speciation? I have already shown that this whole discussion on speciation was an injudicious squander of the energy-draining intellect since speciation is not macroevolution proper. Several successions of speciation events are purported to result in macroevolutionary change, a claim that is demonstrably an unjustified inference.

>> You are saying that all organisms contain DNA switches which allow subgroups to lose their ability to interbreed. That's an awfully large concession you are willing to make. What prevents these these branched subgroups from breeding with one another if they share the same genomes? -Saif

Again, I do not see the relevance of this question to my rebuttal. If you have implied that IDT, if it is a legitimate scientific theory, should have all the answers right away for anything and everything biological, you are mistaken.

Peer-Review

>> And yes, Darwin's Black Box is a popular science book intended for mass consumption. That is an objective statement ? ?Saif

First, let me ask you this. Were Darwin?s The Orign of Species and The Descent of Man peer-reviewed? Were they published in scientific journals?

Second, a history lesson is in order. In the past, heliocentrism and geocentricism used to be battlefields for heated controversy. The controversy took strong foothold with the publication of the heliocentric model that the great astronomer, Nicolaus Copernicus, proposed in his seminal work, De Revolutionibus Orbium Coelestium, in 1543. Was De Revolutionibus Orbium Coelestium peer-reviewed? Einstein failed his entrance examinations in science. Subsequently, during his time as a patent clerk in Baron, Switzerland, he single-handedly wrote famous papers in 1905 on special relativity, Brownian motion, and photoelectric effect, papers a few physicists feel deserved a Nobel Prize. Were those papers peer-reviewed? Gregor Mendel, the ?father of modern genetics,? published in 1865 his Experiments in Plant Hybridization in a relatively unknown German scientific journal Verh. Naturforsch. Ver. Br?nn (Proceedings of the Natural History Society of Brunn) www.mendelweb.org). He read the paper at two meetings of the Natural History Society of Br?nn in 1865. When Mendel's paper was published it had ?little impact and was cited about three times over the next thirty-five years? en.wikipedia.org). His paper was independently discovered by three scientists in 1900 (16 years after his death), yet most biologists treated his work with ?disdain? and ?embryologists saw Mendelism as a threat, systematists considered it an irrelevance, and Darwinians failed to realize how it could be brought into harmony with their view of evolution? www.mendelweb.org). The dispute relentlessly continued, and it was not until the middle of 20th century that his ideas were widely accepted and incorporated into the foundational framework of modern genetics. Today, his portrait is adorned in ?Mendelian Genetics? chapters in most college-level biology textbooks.

Are you able to see the point that I am about to make? If you think that I have relayed a statistically irrelevant sampling of the history of science to imply that the peer-review process is completely useless and that publications in scientific journals hold no merit, I am afraid that you have misunderstood. I will explain why, but to do so I will have to seek a digression in order to describe the nature of ?revolutions.?

Scientific and other revolutions naturally begin with heated controversies largely because human civilizations defy radical reforms of long-established or culturally venerated status quo or the status quo conditioned in the mind-set of the culture through infancy and childhood. That which threatens to wipe out or radically reform the scientific, social, cultural, or theological status quo has encountered furious controversies and even wars throughout the history of human civilizations. A historic example is the dispute over the heliocentric and geocentric models, ignited by the heliocentric model that Copernicus proposed in his seminal work in 1543. The paper may, arguably, be akin to Behe?s Darwin?s Black Box published in 1996. Another more recent example is the half a century long dispute between the Big Bang theory (the universe is finite and was created at a finite point in time) and the steady state theory (the universe is infinite and had no beginning) - one of the great intellectual debates of the 20th century. By the close of the century, the Big Bang theory had eventually gained widespread acceptance and the steady state theory was shoved aside to the burning ashes of history.

Could it be that the contemporary theory of intelligent design is walking the same trail as did the historically contentious Big Bang theory in cosmology? Interestingly, the argumentative framework of the dispute and the opponents? philosophical predisposition to naturalism in the design controversy appear to be strikingly similar to those that have been prevalent in the arguments of the steady state theory in the latter half of the past century. It was considered a flaw (anti-science, pseudo-science, religion, myth, superstition, argument by God or miracle, etc.) in the ?scientific? world to doubt, challenge, or question, even on scientifically justifiable grounds, the unproven axiom that space-time is infinite or eternal. Similar episodes are taking place today in the evolution controversy. To doubt, challenge, or question the unproven axiom that naturalistic mechanisms can produce the information necessary to create novelty or innovation is considered religion, metaphysics, and pseudo-science. As the popular saying goes, ?History repeats,? and I add, ?And human beings seldom seem to learn from their past.?

In my opinion, the design controversy is one of the great debates of the modern era. The controversy may be just the ?tip of the iceberg? of what is yet to come. As the complexities of the cell continue to be unveiled with one research after another, I do not see a valid reason to think that the design approach will never be an accepted paradigm in the sciences in probing the problem of origins, especially given that the Darwinist mechanism continues to encounter difficulties in accounting for the ever-escalating cellular, molecular, and biochemical minutiae. The Big Bang theory was also thoroughly reprimanded with scrupulous scientific criticism and punished with unfounded indictments on philosophical grounds.

Here is the point of the digression. The peer-review process is evidently a great tool in that it subjects an idea to healthy review of expert peers in the field. However, the traditional institutions guarding the peer-review process are inherently a biased roadblock for revolutionary ideas, which have the potential to rattle the very foundational core of knowledge and the personal livelihood of institutional stakeholders. Revolutionary ideas generally constitute a radically new perspective altogether.

Most likely fearing backlash from the traditionalists, Steve Hsu, an associate professor at the University of Oregon, and Tony Zee, a physics professor at the University of California Santa Barbara, explicitly indicated in an article xxx.lanl.gov www.worldscinet.com) published in June 2006 in Modern Physics Letters A the laughably absurd disclaimer that their idea ?does not support the Intelligent Design movement in any way whatsoever,? even though they claim that ?the cosmic microwave background (CMB) provides a stupendous opportunity for the Creator of our universe (assuming one exists) to have sent a message to its occupants, using known physics? (Hsu and Zee 1495). Why would they append such an explicit and absurd disclaimer? Let?s take a quick tour of what happened to a few others who did not make such disclaimers.

Like other proponents of IDT, Guillermo Gonzalez at Iowa State University has been harassed and persecuted in academia (Since a direct link is not coming up on the screen, go here - www.discovery.org - scroll down a bit, and click on ?Dr. Guillermo Gonzalez Responds to Academic Persecution?) for his radical ideas in The Privileged Planet www.amazon.com). Richard Sternberg www.rsternberg.net), editor of the peer-reviewed scientific journal Proceedings of the Biological Society of Washington, was illegitimately indicted, harassed, and accused at the Smithsonian Institution's National Museum of Natural History for publishing, on allegedly creationist and religious grounds, Stephen Meyer?s scientific paper ?The Origin of Biological Information and the Higher Taxonomic Categories.? The preposterous logic of the evolutionary baboons is as follows, ?No peer-reviewed articles have been published in support of IDT. The idea has no support in the scientific world,? and then just as an article is published as demanded, the evolutionist claims, ?Oops, the editor failed to meticulously adhere to the methodology of peer-review. Let?s withdraw the paper!? Incredibly childish behavior!

A plausible reason for the disclaimer in Hsu?s and Zee?s paper should now be easier to envision. Writers seem to be afraid of being harassed for intentionally or unintentionally supporting IDT or seem to be otherwise reluctant to point to an intelligent designer. The environment is not conducive to free revolutionary speech even when backed up with scientific evidence. The traditionalist establishment, strongly opposed to revolutionary propositions that they believe might shatter their careers and financial livelihood, unfortunately dominates the peer-review committees. There is a fearful feeling of unfair prejudice and bullying in the peer-review process of scientific journals.

In light of these outlandish persecutions, harassments, accusations, indictments, and threats, is it fair then to assert and demand the following (see next comment): IDT has published only ?three articles? and that ?ID theorists are not availing themselves to honest scientific pursuit if they cannot put their theories up the test of peer-review?? Is any evolutionist sane enough to publish a paper if the publication entailed the end his career and spelled disaster for his personal livelihood? Are the evolutionists not being childish bullies in town?

Third, unless you have read Behe?s book and his other works or unless you can reach inside Behe?s head to verify his intentions and motivations for writing the book, it is merely your unfounded personal opinion, not an ?objective statement,? that the book is ?intended? for mass consumption.

Absolutely, I expect IDT, like other successful revolutions, to painstakingly walk through the thorny stages of the revolutionary process before reaching the stage of festivity. Otherwise, IDT would not be a revolution. In the long run, it appears that the unfounded rants against design will not prevent the theory from landing a revolutionary footing in the origins research via a purely scientific method. The reason is that it takes a few generations for the elite, dogmatic, and older scientists and professors, whose professional careers and personal livelihood depend on blindfolded adherence to the ideological foundation of their unsupported theories, to die. The brainwashed wider culture, indoctrinated by the elite, powerful, and conventional institutions, also takes time to rot. It takes time, sometimes as long as many centuries, for fresh new thought of youth to discover and to learn the tenets of the revolution. As long as the revolution continues to spread through the masses and successfully keeps winning the young intelligentsia, the unsupported and dogmatic doctrines tend to rot away and the corroborated and the rational notions, ignited by revolutions, eventually take firm hold. Thousands of years of human history has repeated the same phenomena time after time. That in essence is the nature of revolutions.

>> My claim that ID is based largely on public opinion is based on the fact that there are something like (count em) three ID articles published in scientific journals. Obviously ID theorists are not availing themselves to honest scientific pursuit if they cannot put their theories up the test of peer-review. ?Saif

Despite the bias, harassment, and maltreatment in the traditionalist establishment, a scientific revolution should try utmost to subject its ideas to peer-review and to publish articles in scholarly journals. However, the legitimacy of a revolutionary scientific idea is not an exclusive function of the ?count? of peer-reviewed articles published in scientific journals. The legitimacy of a revolution is an intrinsic property of the more vitally important reasoning of the argument and evidence for the proposition itself. Evolutionists have apparently not done their history homework on scientific revolutions.

Despite the cultural turbulence, IDT has published a lot more than just three peer-reviewed articles in scientific journals. An assortment of articles has been published in a wide variety of peer-reviewed scientific and philosophical literature (Since a direct link is not coming up on the screen, go here - www.discovery.org - and click on ?Peer-Reviewed & Peer-Edited Scientific Publications Supporting the Theory of Intelligent Design (Annotated)?).

>> Any scientist will tell you that even fringe theories start there; and if there is some merit to the publication, it will be quoted and referred, and grow in influence. Hence, the theory is not an outgrowth from legitimate scientific inquiry. ?Saif

Refer to the brief history of science above, and then find a scientist who believes that the works of Copernicus, Einstein, and Mendel, to name a few, began with peer-reviewed publications and who believes that today?s scientific understanding of the world is an outgrowth of their illegitimate scientific inquiries.

Purported Evidence for Evolution

>> Re: vestigial organs/atavisms. Check this out: www.livescience.com. IMO, some of these examples are pretty blatantly vestigial (viz. vestigial mating behavior in whiptail lizards, sexual organs on dandelions, wings on flightless birds). These are not mystery organs which we are yet to discover their purpose, but rather decayed versions of once-useful organs. But even more powerful than this is the related issue of atavisms (such as a human tail, or known cases of whales being found with fully formed hindleg atavisms). That is simply inexplicable under the ID paradigm. ?Saif

The argument by vestigial organs is, by definition, an argument from ignorance for which the evolutionists actually hold the proponents of IDT guilty, albeit illegitimately. Let alone refusing to read Behe?s Darwin?s Black Box, you apparently dumped in frenzy the link on the screen without actually reading the material yourself. If you had read item #10 (the very first slide after the cover slide), you should have noted the last sentence, ?The wings are not completely useless, as they are used for balance during running and in flagging down the honeys during courtship displays.? And of course, why could the wings not be used for courtship display? I don?t think I am being unreasonable in demanding that before evolutionists declare certain structures ?vestigial,? they use their creativity (like they do in imagining legendary macroevolutionary transformations) to envisage the possibility that perhaps these birds use their wings to sensually caress or ?hug? members of the opposite sex. Perhaps, the two sexes like to cuddle together with their wings. Perhaps, the wings are used as a voluntarily controlled warming and cooling ?ventilation system? for the undersides of the bird?s body. Therefore, that wings are used only for flight is a biased human construct due to ignorance. Also, it is a philosophical argument that wings in flightless birds are vestigial, ?All wings should be used only for flight. This bird does not fly, yet has wings. Therefore, the wings are vestigial.?

Why should wings be used only for flight? Why should a variety of creative scenarios of wing function other than flight not be plausible hypotheses for further scientific investigation? Why do evolutionists not head out into the field and test the hypotheses? Why do evolutionists throw up their hands and shout, ?Vestigial, vestigial!? prior to further rigorous scientific research? Who has been the science stopper? Who has thrown up their scientific wits in the air in ignorance? Of course, imagining potential scenarios of the structure?s usage is unfavorable for the success of the evolutionary paradigm. After all, evolutionists need ?evidence? that the theory?s predictions have been confirmed and that evolution, in fact, did produce hoards of useless trash.

The crucial point that I want to make is that the allegation that a certain structure is vestigial is a human being?s own biased construct due to lack of scientific knowledge. As proof, the once-hailed, long list of vestigial organs from the time of Darwin has steadily evaporated. Virtually all 19th century ?vestigial? organs have been found to be fully functional systems, indispensable for the survival, reproduction, and multiplication of species.

>> Re: cytochrome C. I forgot to mention the kicker; that progressively dissimilar coding sequences for it (while retaining functionality --- since a large degree of neutral variation IS allowed without destroying functionality) are found for more distantly related species. A clear evidence for the nested heirarchy of organisms. ?Saif

I want to take a detour at this point to the land of phylogenetics. I want to deliberately make reference to the non-biologist evolutionist?s Bible ?29+ Evidences for Macroevolution? written by Douglas Theobald at Talk Origins www.talkorigins.org). I have read this monolithic article, Ashby Camp?s critique at True Origin www.trueorigin.org), and Theobald?s response to Camp. However, judging from the sub-title, a reader is led to believe, if only initially, that Theobald?s monograph supposedly presents a ?scientific case for common descent.? But he has posted a key disclaimer in the Introduction:

?None of the dozens of predictions directly address how macroevolution has occurred, how fins were able to develop into limbs, how the leopard got its spots, or how the vertebrate eye evolved.?

The disclaimer is precisely the issue that IDT contests: a scientific account for the origin of biological information to produce novel features (?how macroevolution has occurred, how fins were able to develop into limbs,? etc.). Furthermore, he states that whether microevolutionary theories (?natural selection, genetic drift, sexual selection, neutral evolution, and theories of speciation?) are sufficient to account for macroevolution is ?a question that is left open.? Thus, Theobald?s presentation appears to be helpless in evaluating the fundamental issue of information and innovation that IDT contests.

In the section Introduction to Phylogenetics, Theobald introduces the ?universal tree of life? (emphasis mine):

?The consensus model which evolutionary biologists use to represent the well-supported branches of the universal tree of life I will refer to as the ?standard phylogenetic tree? ? The macroevolutionary prediction of a unique, historical universal phylogenetic tree is the most important, powerful, and basic conclusion from the hypothesis of universal common descent.?

On January 29, 2007, an electronic version of a to-be-printed scientific journal article ?Pattern pluralism and the Tree of Life hypothesis? was posted at Proceedings of the National Academy of Sciences www.pnas.org). I would like to quote the entire abstract because the point that I want to stress is crucial (emphasis mine):

?Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.?

If there is ?no independent evidence that the natural order is an inclusive hierarchy,? if inclusion of prokaryotes in the tree of life is ?especially problematic,? if data sets used to construct the tree ?often disagree,? if the tree is an ?unproven assumption,? if the tree is ?unlikely to be broadly true,? and if it is better to instead use ?different evolutionary models and representations of relationships? instead of pursuing ?a single true TOL,? then Theobald?s claim is a false proposition, to wit, "The macroevolutionary prediction of a unique, historical universal phylogenetic tree is the most important, powerful, and basic conclusion from the hypothesis of universal common descent." Therefore, there is no such thing as ?universal phylogenetic tree.? And there is no such thing as ?macroevolutionary prediction.?

Since pattern pluralism offers the flexibility to have a variety of trees appropriate to the particular evolutionary models and relationships being studied, the construction of the trees is prone to be influenced by evolutionary predisposition and biased data interpretation. It would then be misleading to say that evolutionists, who are already prone to interpret data to fit theory (e.g., ?vestigial ? organs), have established the plethora of trees with impartial objectivity. And it would be even more misleading to claim that a certain similarity (DNA or amino acid sequences of cytochrome C) across a certain set of supposed evolutionary progression is ?clear evidence for the nested heirarchy of organisms.? Furthermore, since the disagreement is centered on two competing hypotheses (common design and common ancestry), the fact that a certain similarity, homology, or commonality exists in living things is not conclusive evidence in favor of common ancestry and in refutation of common design (See my humorous illustration of this concept in my earlier post ?U.S. Automakers Aim to Standardize Parts?).

>> Re: DNA. How about all the shared genetic errors that have been confirmed to be found in separate species' genomes, such as bits of intersperced viral DNA from past epidemics (there are many more examples of these types of errors). By charting the relative abundance of these shared errors between species, one discovers a nested heirarchy of organisms that aligns perfectly with fossil records.

See the response to the comment above about the purported ?universal tree of life,? which I assume you think aligns ?perfectly? with the fossil record. The theory of evolution is, in fact, at odds with the fossil record, especially with the enigma of the Cambrian Explosion. This is despite the speculatively interpretative rant that many transitional fossils have been found based on the discoveries of many bones and skulls and pieces thereof. I will have to seek another digression to address the fossil record dispute, so I would rather close my response to this comment at this apt juncture.

>> Lastly, I still want to know how you account for this: www.gate.net . ?Saif
>> Obviously you didn't actually read the link about the fused chromosome. The point of the article is not that chimps and humans have nearly identical genomes (which of course they do), but that chromosome 2 in humans is clearly the result of a naturalistic fusion of two chimp chromosomes. This is especially obvious since there are extra nonfunctional remnants of a centromere and two telomeres (from the extra chimp chromosome) still present in the fused human chromosome. Plus, these discoveries were preceded by PREDICTIONS (another important aspect of a scientific theory). -Saif

The testimony of Kenneth Miller, one of the expert witnesses for the plaintiffs at the Dover trial in 2005, touched upon this subject. Miller maintained that common ancestry predicts the fusion event. Casey Luskin wrote an article arguing that the fusion event is by no means a prediction of common ancestry www.ideacenter.org). Luskin also states that the chromosomal fusion event would have most likely resulted in ?non-viable mutant, or non-viable offspring.? One of the well-known instances of chromosomal abnormalities is Down?s syndrome, a human genetic disorder caused by the presence of an extra chromosome 21. Robert Williams in the article that you referenced above argues that ?although they sometimes seem to lead to reduced fertility, this is often not the case.? And then he cites three references about mice, cattle, and sheep to show that chromosomal abnormalities do not always result in infertile offspring. He assures that he can present ?many more similar references? if requested. But that does not necessarily validate the claim that the one particular naturalistic, ancestral ape chromosomal fusion that supposedly led to the evolution of Homo Sapiens produced viable and fertile offspring. It may very well have not produced viable and fertile offspring as Williams admits that ?the horse and the donkey produce an infertile mule in crossing because of a different number of chromosomes in the two species.? Even if the chromosomal abnormalities are ?often? harmless as Williams maintains, faith in such a grand decree that humans naturalistically evolved from apes still rests on which side of the evidence you lean on (the cases where chromosomal abnormalities produce infertile offspring or the cases where the abnormalities are seemingly harmless).

I would like to respond to an instructive lesson posted at Indiana University in regards to human chromosome 2 and its alleged naturalistic fusion from two ape chromosomes www.indiana.edu). The lesson poses the question, ?Why does our chromosome #2 appear to be so very similar to the two shorter chromosomes found in apes (chimpanzees, gorillas, and orangutans)?? Next, it builds three ?working hypotheses? about the human and ape chromosomes at issue:

?1. They were designed that way.
2. Chromosome 2 split into two (fission) in the ancestral branch (or branches) that produced the apes.
3. Chromosome 2 formed from the joining (fusion) of two shorter chromosomes in an early human ancestor after the apes branched off.?

It then simply makes the following dogmatic assertion or, to use your own terminology from your comment on 9/14/05, a ?tandard vacuous argument from incredulity?:

?To suggest ?design? as an explanation usually implies a supernatural designer, and since supernatural forces cannot be reliably tested or disproved (basic requirement for all scientific explanations), ?design? cannot be properly considered as a scientific explanation.?

The possibility of intentional design is, thus, eliminated, and hypothesis #3 is pinned down as the most likely cause. Such a dogmatic analysis throws us back to square one: the very contentious issue at sake of whether IDT, in fact, is science, can be tested, and relies on the supernatural. Is that not the very issue at stake? Therefore, it is a rather circular argument to blindly rule out the design hypothesis, which is the issue on the table, ?pick and choose? hypothesis #3 as the most likely explanation, and then come back around and assert, ?The fusion event is evidence of common ancestry.?

The inverted telomeric sequences in the centromere region of human chromosome 2 are not ?clearly the result of a naturalistic fusion.? Why couldn?t the designer have gathered the raw materials to first initiate an engineering baseline with the genetic blueprint (DNA and chromosomes) of a primate species or a blueprint similar to that of a primate?s, and then why couldn?t the designer have tinkered with phase 1 of the design (i.e., joined two chromosomes head-to-head) to create the genetic blueprint of the human species? In such a process the designer could have simply fused the two primate chromosomes, the functions of the genes of which may well be indispensable for humans also, into a new chromosome for humans. That is the characteristic nature of engineering. I am an engineer by profession. Go take a peek into the engineering offices, labs, and research centers around the globe: IBM, Intel, Microsoft, Nokia, Cisco, Juniper Networks, Toyota, DaimlerChrysler, Panasonic, Logitech, NVIDIA, wireless Bluetooth technology companies, to name a few designers. Aren?t certain components of driveshafts (shafts that transfer power from the engine and transmission to the differential axles of vehicles) of certain passenger models ?fused? or welded together with other parts to design shafts for other vehicle platforms like SUVs or vans that may require higher torques based on certain engineering parameters such as vehicle weight? Do Microsoft and software programmers not ?fuse? or combine certain lines of code or could they not do so to design Windows Vista from the software blueprint of Windows XP? Does Intel not release new microprocessor designs based on modifications to existing microprocessor hardware architecture? Did AMD Athlon never design or could it not design its microprocessor?s printed circuit boards with certain electronic components ?fused? or soldered together?

Are chromosomal fusions, inversions, and translocations in humans and primates necessarily evidence for naturalistic mechanism and refutation of intentional design? Why? It is a philosophical argument that one or more than one designer should not have, would not have, could not have, or may not have intentionally fused, inverted, translocated, or juggled certain biochemical and genetic elements of an existing species (Intel Pentium IV HT microprocessor) to engineer new species (Intel Pentium IV Extreme Edition microprocessor) en.wikipedia.org).

>> Lastly, what of atavisms? For the third time, HOW do you account for atavisms? -Saif

For the second time, the argument by vestigial organs is, by definition, an argument from ignorance. So is the case with atavisms. Why could the atavisms (hind legs on whales, hind limbs on dolphins, extra toes on horses) not be unavoidable relics of essential morphological transformations during embryological development? I am really excited to research this prospect because I want to promote the cause of scientific advancement. Do you want to be a part of this? Or, would you want to throw up your scientific wits in frenzied excitement, ?Vestigial! Atavism! Evolutionary garbage! Confirmation of prediction!? Do you want to be a science stopper?

I may respond to a few other key objections in Part 2 of the rebuttal.

Nadeem

References (excludes references to user-edited Wikipedia.org encyclopedia)

Campbell, Neil A., and Jane B. Reece. Biology. San Francisco: Benjamin Cummings, 2002.

Chromosome Fusion. Evolution and Nature of Science Institute, Indiana University. 3 February 2007 www.indiana.edu).

Dodd, Diane M.B. "Reproductive isolation as a consequence of adaptive divergence in Drosophila pseudoobscura." Evolution 43 (1989): 1308?1311.

Doolittle, Ford W, and Eric Bapteste. ?Pattern pluralism and the Tree of Life hypothesis.? Proceedings of the National Academy of Sciences, 10.1073/pnas.0610699104 (published online before print January 29 2007) www.pnas.org).

Hsu, S, and A Zee. ?Message in the Sky.? Modern Physics Letters A 21.19 (2006): 1495-1500 xxx.lanl.gov www.worldscinet.com).

Luskin, Casey. And the Miller Told His Tale: Ken Miller's Cold (Chromosomal) Fusion. Intelligent Design and Evolution Awareness Center. 4 February 2007 www.ideacenter.org).

Mendel, Gregor. ?Versuche ?ber Pflanzen-Hybriden.? Verh. Naturforsch. Ver. Br?nn 4 (1866): 3?47 (translated to English by Journal of the Royal Horticultural Society 26 (1901): 1?32) www.mendelweb.org).

Meyer, Stephen C. ?The Origin of Biological Information and the Higher Taxonomic Categories.? Proceedings of the Biological Society of Washington 117.2 (2004): 213-239.

Olby, Robert C. ?Mendel, Mendelism and Genetics.? Department of the History and Philosophy of Science at University of Pittsburgh. 1997. 3 February 2007 www.mendelweb.org).

Williams, Robert. Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry. The Evolution Evidence Page. 4 February 2007 www.gate.net).